[R] APE

[Simon Blomberg]

It's hard to tell what you did exactly. Did you do:

mytree <- compute.brlen(mytree)

? That should have worked. I've cc'ed this message to r-sig-phylo, which 
is the more appropriate forum.

Cheers,

Simon.

On 10/03/15 07:05, Beth Williams wrote:
> Dear All,
>
>
> I am having some trouble with R and would be extremely grateful if anyone has a way around this. I have loaded a nexus tree from PAUP into R using the command read.nexus and this loaded,  it was reported as "rooted; with no branch lengths". I then used the command "compute.brlen(mytree)" to compute the branch lengths and this was reported as "rooted; includes branch lengths". I added my community data (samp) and then tried to compute the phylogenetic diversity with the command "> pd(samp, mytree, include.root=TRUE)" however it said it could not calculate the PD as there were no branch lengths. Is there a way to incorporate the branch lengths into the calculation for PD?
>
>
> Thanks for your time,
>
> Beth
>
> 	[[alternative HTML version deleted]]
>
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-- 
Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat.
Senior Lecturer and Consultant Statistician
School of Biological Sciences
The University of Queensland
St. Lucia Queensland 4072
Australia
T: +61 7 3365 2506
email: S.Blomberg1_at_uq.edu.au
http://www.evolutionarystatistics.org

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